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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.510421169648422

Latest revision as of 12:45, 17 September 2013


Full id: C4430_CD14_Neutrophils_mesenchymal_Smooth_Mast_Whole_large



Phase1 CAGE Peaks

Hg19::chr4:80994351..80994402,-p1@ANTXR2
Hg19::chr4:80994415..80994426,-p11@ANTXR2
Hg19::chr4:80994471..80994485,-p7@ANTXR2


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
somatic stem cell6.16e-28433
multi fate stem cell1.43e-27427
stem cell2.32e-27441
myeloid leukocyte5.69e-2672
myeloid cell1.10e-24108
common myeloid progenitor1.10e-24108
classical monocyte2.10e-2442
CD14-positive, CD16-negative classical monocyte2.10e-2442
hematopoietic stem cell5.47e-24168
angioblastic mesenchymal cell5.47e-24168
granulocyte monocyte progenitor cell9.31e-2367
leukocyte1.29e-22136
hematopoietic oligopotent progenitor cell1.76e-22161
hematopoietic multipotent progenitor cell1.76e-22161
hematopoietic cell2.56e-22177
monopoietic cell1.22e-2159
monocyte1.22e-2159
monoblast1.22e-2159
promonocyte1.22e-2159
defensive cell1.48e-2148
phagocyte1.48e-2148
myeloid lineage restricted progenitor cell4.48e-2166
connective tissue cell6.17e-21361
macrophage dendritic cell progenitor6.98e-2161
mesenchymal cell8.20e-21354
nongranular leukocyte1.18e-17115
hematopoietic lineage restricted progenitor cell1.70e-17120
motile cell7.25e-15386
somatic cell2.78e-13588
vascular associated smooth muscle cell3.60e-1032
stuff accumulating cell2.20e-0987
smooth muscle cell1.28e-0843
smooth muscle myoblast1.28e-0843
muscle cell3.64e-0855
muscle precursor cell4.38e-0858
myoblast4.38e-0858
multi-potent skeletal muscle stem cell4.38e-0858
contractile cell4.93e-0859
native cell9.16e-07722
Uber Anatomy
Ontology termp-valuen
musculoskeletal system2.05e-21167
connective tissue3.01e-20371
mesoderm5.48e-20315
mesoderm-derived structure5.48e-20315
presumptive mesoderm5.48e-20315
bone marrow1.61e-1976
hematopoietic system1.80e-1998
blood island1.80e-1998
bone element5.57e-1882
skeletal element1.49e-1790
lateral plate mesoderm7.85e-17203
hemolymphoid system2.99e-16108
immune system2.44e-1593
skeletal system7.84e-15100
muscle tissue1.18e-0764
musculature1.18e-0764
musculature of body1.18e-0764
skeletal muscle tissue2.72e-0762
striated muscle tissue2.72e-0762
myotome2.72e-0762
artery7.02e-0742
arterial blood vessel7.02e-0742
arterial system7.02e-0742


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.10.178364
MA0004.10.826076
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.11.89908
MA0043.11.32783
MA0046.11.31611
MA0048.11.62115
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.886807
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.990225
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.11.3784
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.13.75836
MA0144.10.531867
MA0145.11.37817
MA0146.13.00132
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.62945
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.21.34467
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.181755
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CCNT2#90536.336201576962630.003930750035764890.0190781486655474
E2F6#187635.017155731697390.00791769806886330.0323747736517897
EGR1#195834.988179094810140.008056488137383440.0321948178526952
ELF1#199734.258097958807540.01295179875054610.0464245773315126
EP300#203336.77394172622320.003216880500103790.0168093151823855
FOS#235338.99795530889440.001372499272417130.00900561987258733
FOSL1#8061339.7135797163731.59554825631833e-050.000372124752884391
GATA2#2624312.7449317335540.0004829527704283790.00438296006176308
HMGN3#932438.178547723350590.001827766942164210.0109017790789656
IRF1#365937.63716375356390.002244692747297240.0128562361302428
JUND#372736.994663941871030.002921845042734990.0157361063540738
MXI1#460139.96157162875930.001011470541259020.00722155946530975
NRF1#4899312.21027944771090.0005492172401020010.0047279673045675
RAD21#5885310.35503389545630.0009004912073565420.00667043061246257
REST#597839.650028716128020.001112636247114590.00770114765805558
SIN3A#2594235.408884726815140.006318961977991520.0277836934290177
SP1#666735.69838137814090.005403962701712170.0247526187712871
SPI1#668838.204323508522730.001810593189410520.0109323317401194
TFAP2A#7020316.5186343730450.0002218033880766340.00249138783042972
TFAP2C#7022310.80922860986020.0007916746575753130.00617996184785919
TRIM28#10155318.59052504526250.0001555969297255280.00197669234200272



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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